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At least 127 records · Page 7Linked to original sources
PubMed1999

Phylogenetic signal in the COI, 16S, and 28S genes for inferring relationships among genera of Microgastrinae (Hymenoptera; Braconidae): evidence of a high diversification rate in this group of parasitoids.

The subfamily Microgastrinae is a highly diversified group of parasitoid wasps that attacks all of the different groups of Lepidoptera. We explore here the phylogenetic signal in three gene (mitochondrial COI and 16S, and nuclear 28S) fragments as an assessment of their utility in resolving generic relationships within this species-rich insect group. These genes were chosen because their level of sequence divergence is thought to be appropriate for this study and because they have resolved relationships among other braconid wasps at similar taxonomic levels. True phylogenetic signal, as opposed to random signal or noise, was detected in the 16S and 28S data sets. Phylogenetic analyses conducted on each microgastrine data set, however, have all resulted in poorly resolved trees, with most clades being supported by low bootstrap values. The phylogenetic signal, if present, is therefore concentrated on a few well-supported clades. Some rapidly evolving sites may be too saturated to be phylogenetically useful. Nonetheless, the sequence data (nearly 2300 nucleotides) used here appear to exhibit the appropriate level of variation, theoretically, to resolve the relationships studied. Moreover, the clades that are well supported by the data are usually supported by more than one data set and represent different levels of sequence divergence. We suggest that the lack of phylogenetic signal observed is an indication of the presence of many short internal branches on the phylogeny being estimated, which in turn might be the result of a rapid diversification of the taxa examined. Relative specialization of diet, which is typically associated with parasitic behavior, is believed to result in high radiation rates, which may have been especially high in microgastrine wasps because of the great diversity of their lepidopteran hosts. This hypothesis of a rapid diversification caused by an abundance of host species remains speculative and more data will be needed to test it further.

Algorithms↗
PubMed2000

Homeobox gene diversification in the calcareous sponge, Sycon raphanus.

Knowledge of the developmental mechanisms in living basal metazoan phyla is crucial for understanding the genetic bases of morphological evolution in early animal history. We looked for homeobox genes in the calcareous sponge, Sycon raphanus, using the polymerase chain reaction. Partial sequences of eight homeoboxes were recovered, five of which are assignable to the NK-2 class of homeoboxes. The three remaining sequences are related members of a new class of homeoboxes, the Sycox class, showing limited similarity to bilaterian Lbx, Hlx, HEX, En, and Cad classes. Among the five NK-2 class homeoboxes are four closely related sequences occupying a divergent position within the class, the remaining one on the contrary showing high sequence similarity with members of the NK-2 family, a particular subgroup within the NK-2 class, previously known only from the Bilateria. This suggests that diversification of the NK-2 class occurred early in metazoan history. Altogether, the results reveal an unexpected diversification of homeobox genes in S. raphanus.

Amino Acid Sequence↗
PubMed2001

Rapid diversification of RNase A superfamily ribonucleases from the bullfrog, Rana catesbeiana.

We present sequences of five novel RNase A superfamily ribonuclease genes of the bullfrog, Rana catesbeiana. All five genes encode ribonucleases that are similar to Onconase, a cytotoxic ribonuclease isolated from oocytes of R. pipiens. With amino acid sequence data from 14 ribonucleases from three Rana species (R. catesbeiana, R. japonica, and R. pipiens), we have constructed bootstrap-supported phylogenetic trees that reorganize these ribonucleases into five distinct lineages--the pancreatic ribonucleases (RNases 1), the eosinophil-associated ribonucleases (RNases 2, 3, and 6), the ribonucleases 4, the angiogenins (RNases 5) and the Rana ribonucleases--with the Rana ribonucleases no more closely related to the angiogenins than they are to any of the other ribonuclease lineages shown. Further phylogenetic analysis suggests the division of the Rana ribonucleases into two subclusters (A and B), with positive (Darwinian) selection (dN/dS > 1.0) and an elevated rate of radical nonsynonymous substitution (dR) contributing to the rapid diversification of ribonucleases within each cluster. This pattern of evolution-rapid diversification via positive selection among sequences of a multigene cluster-bears striking resemblance to what we have described for the eosinophil-associated ribonuclease genes of the rodent Mus musculus, a finding that may have implications with respect the physiologic function of this unique family of proteins.

Amino Acid Sequence↗
PubMed2001

Zebrafish hybrids suggest genetic mechanisms for pigment pattern diversification in Danio.

Pigment patterns of Danio fishes are a tractable system for assessing the developmental genetic bases for the evolution of adult form in vertebrates. These pigment patterns include multiple horizontal melanophore stripes in the zebrafish D. rerio, a complete absence of stripes in D. albolineatus, a few broad stripes in D. kerri, and a combination of stripes and spots in D. nigrofasciatus. Here we assess the genetics of pigment pattern development and evolution using interspecific hybrids. We first reconstruct the phylogenetic relationships of these species by analyzing mitochondrial 12S and 16S rDNA sequences. We find a clade comprising several small species of danio, and within this clade a sister taxon relationship between D. rerio and D. nigrofasciatus. We also find that the large bodied D. dangila is more closely related to the clade of small danios than other large bodied species. As a first step in evaluating the genetics of pigment pattern diversification in the group, we then examine the phenotypes of interspecific hybrids. Adult pigment patterns of hybrids between D. rerio and other danios are in many respects more similar to D. rerio than the heterospecific danio, demonstrating that alleles of pigment pattern genes in other species typically are recessive to D. rerio alleles. Furthermore, hybrids between two additional striped species (D. kerri, D. nigrofasciatus) and D. albolineatus suggest that striped patterns are dominant or semi-dominant over an absence of stripes. Together, these analyses support a model in which pigment pattern differences between D. rerio and other species result from gain-of-function alleles in D. rerio, or loss-of-function alleles in other danios. Finally, because several D. rerio pigment pattern mutants resemble heterospecific danios, we use interspecific complementation tests to assess potential roles for these loci in pigment pattern diversification. Crosses between other danios and most D. rerio pigment pattern mutants develop stripes, similar to control hybrids with wild-type D. rerio. These complementation phenotypes allow us to exclude most of these loci as having major effect roles in generating pigment pattern differences between species. In contrast, hybrids between fms mutant D. rerio and D. albolineatus fail to develop stripes, similar to D. albolineatus. This non-complementation phenotype identifies changes in fms, or the pathway in which it acts, as candidates for contributing to the evolutionary loss of stripes in D. albolineatus.

Animals↗
PubMed2001

Linking specialisation to diversification in the Diplectanidae Bychowsky 1957 (Monogenea, Platyhelminthes).

The hypothesis of a positive correlation between host specificity and taxonomic diversification was tested in a family of fish ectoparasites, the Diplectanidae Bychowsky 1957 (Monogenea). A comparative analysis of correlation of species richness with host specificity was performed using an adapted independent contrasts method. In order to control for phylogenetic effects, a phylogenetic tree of the genera in the Diplectanidae was reconstructed using morphological characters. The current taxonomy is retrieved in this phylogenetic hypothesis, except for the Murraytrematoidinae subfamily, which appears to be paraphyletic. There is no significant correlation between host specificity and taxonomic diversification in the Diplectanidae. The significance of this result is discussed, and different hypotheses which could have led to this observation are presented.

Animals↗
PubMed2005

Maintenance of cell type diversification in the human breast.

Recent genome-wide expression analysis of breast cancer has brought new life to the classical idea of tumors as caricatures of the process of tissue renewal as envisioned by Pierce and Speers (Cancer Res 1988;48:1996-2004) more than a decade ago. The search for a cancer founder cell or different cancer founder cells is only possible if a hierarchy of differentiation has been established for the particular tissue in question. In the human breast, the luminal epithelial and myoepithelial lineages have been characterized extensively in situ by increasingly elaborate panel of markers, and methods to isolate, culture, and clone different subpopulations have improved dramatically. Comparisons have been made with the mouse mammary gland in physiological three-dimensional culture assays of morphogenesis, and the plasticity of breast epithelial cells has been challenged by immortalization and transformation. As a result of these efforts, several candidate progenitor cells have been proposed independently of each other, and some of their features have been compared. This research has all been done to better understand breast tissue homeostasis, cell-type diversification in general and breast cancer evolution in particular. The present review discusses the current approaches to address these issues and the measures taken to unravel and maintain cell type diversification for further investigation.

Animals↗
PubMed2006

Structure based studies of the adaptive diversification process of congerins.

The isoforms of a fish galectin, congerins I and II, have several features that make them suitable for a study of accelerated process of molecular diversification based on 3D structures: They have been generated by a gene duplication, and still maintain 47% amino acid sequence identity to each other. Their genes show very high K A: /K S: ratio, and are though to be components of fish defense system. The crystal systems for a high-resolution analysis are known for both proteins. A series of works with biochemistry, molecular biology, and X-ray crystallography techniques have suggested that the two proteins might have evolved under differential selection pressures. Congerin I appeared to be a stabilized version of galectin-1. Congerin II was shown to be adapted to a new carbohydrate-ligand. The 3D structures of the wild type and mutant proteins have revealed the probable cause and consequence of the selection pressure responsible for the diversification of congerins.

Adaptation, Physiological↗
PubMed1990

Somatic diversification of immunoglobulin heavy chain VDJ genes: evidence for somatic gene conversion in rabbits.

Rabbits preferentially utilize only one of their multiple functional germline immunoglobulin VH genes. This preferential usage of one gene, VH1, raises the question of how rabbits generate antibody diversity. VDJ diversification was analyzed by cloning and sequencing VH1 gene rearrangements. Comparison of these sequences with that of germline VH1 identified clusters of nucleotide changes, including codon insertions and deletions. To investigate whether gene conversion was involved in this somatic diversification, we searched a data base of rabbit germline VH gene sequences for donor VH genes; potential donors were identified for five diversified regions. We conclude that somatic gene conversion has a major role in generating antibody diversity in rabbits. These studies provide clear evidence for somatic gene conversion of mammalian VDJ genes.

Animals↗
PubMed2026

Evolutionary architecture and lineage-specific diversification of Forkhead box transcription factors in Perna viridis.

The Forkhead box (Fox) transcription factors are evolutionarily conserved regulators of development, cell cycle, and apoptosis across metazoans. This study provides the first comprehensive genome-wide analysis of the Fox gene family in the Asian green mussel (Perna viridis). We identified 28 Fox genes distributed across 10 chromosomes. Comparative analysis reveals the absence of the FoxI, FoxQ1, FoxR and FoxS subfamily, consistent with other bivalves and indicative of lineage-specific gene loss during molluscan evolution. Notably, gene duplications in the FoxAB, FoxD, FoxH, FoxN1-4, FoxQ2 and FoxQD subfamilies may reflect functional diversification associated with environmental adaptation. Exon-intron structural variability, including intron loss in several paralogues, suggests structural diversification and potential regulatory variation. Phylogenetic reconstruction confirmed the monophyly of core Fox classes while highlighting divergent expansion patterns in lophotrochozoans. Selection analyses showed strong purifying selection across duplicated Fox paralogs, supporting functional conservation after lineage-specific expansion. Gene Ontology enrichment linked Fox genes to stress response, apoptosis, and transcriptional regulation. By integrating phylogenetic, structural, and transcriptomic analyses, this study provides a genomic framework for understanding Fox gene organisation, evolution, and tissue-associated expression patterns in Perna viridis and establishes a comparative resource for future functional studies in bivalves.

Animals↗
PubMed2004

Immunoglobulin diversification in DT40: a model for vertebrate DNA damage tolerance.

Studies of recombination in vertebrates have rather lagged behind those in yeast and bacteria in large part due to the relative genetic intractability of vertebrate model systems. Immunoglobulin diversification in the chicken cell line DT40 provides a powerful combination of a physiological recombination process coupled with facile genetic modification. The immunoglobulin variable regions of DT40 constitutively diversify by a combination of gene conversion, in which sequence changes are templated from one of a number of upstream pseudogenes or by non-templated point mutation. Both of these events are initiated by abasic sites in the variable region DNA generated following the targeted deamination of cytidine by activation induced deaminase. Recent work has shown that the two outcomes, gene conversion and somatic mutation, are likely to reflect alternate pathways for the processing of these abasic sites. In this review I will discuss the current data on avian Ig gene diversification and examine how the immunoglobulin loci of DT40 may provide a useful model system for studying the mechanisms and interactions of vertebrate recombination and pathways of DNA damage tolerance.

Animals↗
PubMed2005

Flower development and evolution: gene duplication, diversification and redeployment.

Gene duplication and diversification can provide the raw material for the evolution of new morphologies. In plants, the numbers of MADS-box genes have multiplied considerably, resulting in a plethora of these transcriptional regulators in the angiosperms (flowering plants). MADS-box genes have been implicated in the regulation of a variety of flower developmental processes; therefore, understanding the functional consequences of duplication and diversification in this gene family can shed light on the evolution of different floral forms. Recent functional analyses of MADS-box gene lineages have demonstrated that in various instances these genes have swapped roles, acquired novel roles, or retained ancestral roles. These studies underscore the idea that gene function cannot be extrapolated from structural orthology.

Evolution, Molecular↗
PubMed2005

The catalytic activity of REV1 is employed during immunoglobulin gene diversification in DT40.

REV1 plays a key role in vertebrate translesion synthesis. Although its deoxycytidyl transferase activity is dispensable for tolerance of DNA damage caused by a number of mutagens, its extreme C terminus, which interacts with other translesion polymerases and PCNA, is essential. By examining immunoglobulin diversification in the genetically tractable chicken cell line DT40 we show that the generation of non-templated point mutations from C/G to G/C does require the catalytic activity of REV1. This provides the first clear evidence that the catalytic activity of REV1 is utilised in vivo in higher eukaryotes and is involved in immunoglobulin diversification. Although rev1 DT40 cells incorporate few point mutations, a mutant lacking the C terminus of REV1 exhibits a similar level to that seen in wild-type cells. Thus, the polymerase selection or stabilisation role of REV1 does not appear to play a major role in the bypass of AID-dependent abasic sites.

Animals↗
PubMed2004

Molecular studies on the diversification of hemagglutinin-specific human neonatal repertoire subsequent to immunization with naked DNA.

It is well known that newborns and infants respond poorly to immunization with influenza virus vaccines. The poor response of neonates may be related to restricted B cell repertoire and high susceptibility of neonates to high dose tolerance. Protective antibody response against hemagglutinin (HA) of influenza virus is a T-dependent response. While the immunization of neonates with live virus caused a long lasting unresponsiveness, the immunization with a plasmid containing influenza virus HA circumvents the neonatal unresponsiveness. Genetic immunization primes efficiently neonatal HA-specific B cells, and induces memory cell enabling the animals to develop a strong secondary response and to survive to challenge with a lethal dose. The most striking effect of neonatal immunization consists of a shift of neonatal HA-specific B cell repertoire to adult-type as assessed by analysis of reactivity pattern of HA-specific clonotypes. The diversification is associated with the induction of germinal centers, increased number of B220(+)GL-7(+) cells and with the re-expression of RAG genes. This suggests that the receptor revision may contribute to the diversification of HA-specific neonatal B repertoire.

Animals↗
PubMed2006

The sympathoadrenal cell lineage: specification, diversification, and new perspectives.

During the past years considerable progress has been made in understanding the generation of cell diversity in the neural crest (NC). Sympathoadrenal (SA) cells constitute a major lineage among NC derivatives; they give rise to sympathetic neurons, neuroendocrine chromaffin cells, and the intermediate small intensely fluorescent (SIF) cells. The classic perception of how this diversification is achieved implies that (i) there is a common progenitor cell for sympathetic neurons and chromaffin cells, (ii) NC cells are instructed to a SA cell fate by signals derived from the wall of the dorsal aorta, especially bone morphogenetic proteins (BMP), and (iii) the local environments of secondary sympathetic ganglia and adrenal gland, respectively, are crucial for inducing differentiation of SA cells into sympathetic neurons and adrenal chromaffin cells. However, recent studies have suggested that the adrenal cortex is dispensable for the acquisition of a chromaffin cell fate. This review summarizes the current understanding of the development of SA cells. It covers the specification of SA cells from multipotent NC crest cells, the role of transcription factors during their development, the classic model of their subsequent diversification as well as alternative views for explaining the generation of endocrine versus neuronal SA derivatives.

Adrenal Glands↗
PubMed2004

Temporal diversification of Mesoamerican cichlid fishes across a major biogeographic boundary.

The Mexican Neovolcanic Plateau sharply divides the vertebrate fauna of Mesoamerica where the climate of both the neotropics and temperate North America gradually blend. Only a few vertebrate groups such as the Heroine cichlids, distributed from South America to the Rio Grande in North America, are found both north and south of the Neovolcanic Plateau. To better understand the geography and temporal diversification of cichlids at this geologic boundary, we used mitochondrial DNA sequences of the cytochrome b (cyt b) gene to reconstruct the relationships of 52 of the approximately 80 species of Heroine cichlids in Mesoamerica. Our analysis suggests several cichlids in South America should be considered as part of the Mesoamerican Heroine clade because they and the cichlids north of the Isthmus of Panama are clearly supported as monophyletic with respect to all other Neotropical cichlids. We also recovered a group containing species in Paratheraps+Paraneetroplus+Vieja as the sister clade to Herichthys. Herichthys is the only cichlid clade north of the Mexican Plateau and it is monophyletic. Non-parametric rate smoothing of cichlid cyt b sequence resulted in an estimated divergence time of approximately 6 million years for Herichthys. This temporal diversification is concordant with divergence times estimated for anurans in the genus Bufo, a group that exhibits a similar geographic distribution. Our results indicate the 5-million-year-old extension of the Mexican Neovolcanic Plateau to the Gulf Coast of Mexico has strongly influenced the current transition between the vertebrate faunas of the Neotropics and Nearctic.

Animals↗
PubMed2005

Phylogeny and age of diversification of the planitibia species group of the Hawaiian Drosophila.

The Hawaiian Drosophila offer a unique opportunity to examine evolutionary questions because of the known ages of the Hawaiian Islands and the large number of species endemic to this archipelago. One of the more well studied groups of Hawaiian Drosophila is the planitibia species group, a long-standing population genetic model system. Here we present a molecular phylogenetic hypothesis of all 17 taxa in the planitibia group based on nucleotide sequences from two mitochondrial (16S and COII) and four nuclear (Adh, Gpdh, Yp1, and Yp2) loci, accounting for over 4kb of sequence per taxon. We use these data to estimate major divergence times within this group. Our results suggest that the basal diversification within this group, calculated at 6.1 +/- 0.47 MY, predates the oldest high island of Kauai. The older diversifications in this group took place on Kauai, with subsequent colonization and speciation events occurring as new islands became available to Drosophila. Understanding of the phylogenetic relationships of this important group will place the existing population genetic work in a macroevolutionary context and stimulate additional work, particularly on those taxa endemic to the Maui Nui complex of islands.

Animals↗
PubMed2005

Local origin and diversification among Lampornis hummingbirds: a Mesoamerican taxon.

The huge biodiversity found in Mesoamerica is often explained by its geographic situation as a natural bridge between two large biogeographic regions. Often overlooked, however, are the high levels of speciation and diversification in the area. Here we assess the phylogenetic relationships within a Mesoamerican group of hummingbirds (Lampornis). We sequenced both mtDNA (1,143 bp of cyt b and 727 bp of ND5) and nuclear genes (505 bp of AK-5 intron and 567 bp of c-mos) for each of the seven recognised species and outgroups. We find two or three clades of similar age within this genus: L. clemenciae and L. amethystinus (singly or as each other's sister taxa) and a Central American clade. This Central-American clade presents a clear bipartition between northern (L. viridipallens and L. sybillae) and southern Mesoamerica, which is shared with many other Mesoamerican organisms. Our analyses suggest that L. hemileucus does not belong in the genus Lampornis. While we refrain to apply a time-scale to our data because of the lack of an appropriate calibration, our results indicate that the genus Lampornis predates the uprising of the Panama land-bridge, and that diversification among the isthmian species (L. castaneoventris and L. calolaema) is a very recent event. Our results strongly suggest a local Mesoamerican origin for this genus.

Animals↗
PubMed2006

Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): phylogenetic tests of fossil-based hypotheses.

Pines comprise one of the largest coniferous genera, are distributed throughout the Northern Hemisphere, and have an abundant fossil record. Distributions of fossils have been used to derive a three-step hypothesis of early pine evolution, which postulates a Mesozoic origin for the genus, east-west expansions across Laurasia, and retraction into Eocene refugia. Here, we present phylogenetic tests of this hypothesis using chloroplast sequence data from four loci for 83 pine species. We used the fossil-based hypothesis to derive null expectations concerning monophyly of taxonomic groups, dates of cladogenesis, and patterns of diversification. Phylogenetic analyses using several algorithms subsequently provided rigorous tests of these expectations. Our inferred phylogenies illustrated broad congruence with taxonomic groups, but highlighted consistent problems within subgenus Strobus. Estimated minimum dates of divergence derived from relaxed clock methods were largely consistent with the fossil record and yielded a date for the ingroup node of Pinus of 128+/-4 mya, depending upon the calibration used for subgenus Pinus. Ancestral area reconstructions showed Pinus to have most likely originated in Eurasia. Major clades differed in biogeographic patterns, but were consistent with the fossil-based hypothesis. We found weak support, however, for a change in diversification rate in the Eocene as interpretations of fossil distributions would have predicted.

Fossils↗